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Crystal Structure of VHH MOD225 in complex with SARS-CoV-2 KP.3 RBD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QH1 experimental model PDB 9G48
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.2 M Sodium Iodide; 17.5% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.36 63.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.953 α = 90 b = 85.953 β = 90 c = 120.948 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 XE 9M 2024-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.97856 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.35 46.94 100 0.15 0.994 15.2 19.6 22124
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.43 100 3.811 0.354 0.9 20.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.35 46.94 20975 1115 99.98 0.20583 0.20417 0.2066 0.2383 0.2379 RANDOM 71.351
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.31 0.15 0.31 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.477 r_dihedral_angle_3_deg 15.452 r_long_range_B_other 10.929 r_long_range_B_refined 10.925 r_scangle_other 9.342 r_dihedral_angle_1_deg 6.522 r_scbond_other 6.475 r_scbond_it 6.47 r_mcangle_other 6.131 r_mcangle_it 6.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.477 r_dihedral_angle_3_deg 15.452 r_long_range_B_other 10.929 r_long_range_B_refined 10.925 r_scangle_other 9.342 r_dihedral_angle_1_deg 6.522 r_scbond_other 6.475 r_scbond_it 6.47 r_mcangle_other 6.131 r_mcangle_it 6.124 r_mcbond_it 4.522 r_mcbond_other 4.514 r_angle_refined_deg 1.668 r_angle_other_deg 0.555 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2531 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction